Maximilian Haeussler wrote:
Hi,
I have discovered a little inconsistency in biomart.
Usually, the orthologs between two species are stored in a mart called
compara_speciesx_speciesy_orthologs, where speciesx and speciesy are
sorted alphabetically.
There is at least one exception: fly-zebrafish orthologs are stored in
compara_drer_dmel instead of compara_dmel_drer.
( You aren't creating all these databases manually, are you?? :-) )
Maximilian,
Indeed the species names should be sorted alphabetically, like you said
speciesX_speciesY
I will investigate this, and get back to you as soon as possible.
Benoit
I'm using scripts that access biomart, so I've stumbled over this and
added various "if...then"s as a walkaround in my scripts.
cheers,
Max
--
Benoit Ballester, PhD
Ensembl Team
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, United Kingdom
